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I was just curious about this. The BCL files (~100GB) we have for a single cell experiment (10x chromium), are less than half the size of the produced fastq files (240GB, gzipped). This is excluding the uncharacterized reads fastqs.

Is this usual? All other types of sequencing data demultiplexes do not have this increase in file size. Is this because there are 4 fastqs per sample (indexes and reads).

Thanks in advance,

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I do not have direct experience with BCL, so this is just a guess. FASTQ is text-based, while BCL is in binary format and probably optimized to be efficiently stored. The conversion BCL2FASTQ might require some filtering. The level of compression can also be a factor.

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  • $\begingroup$ yes, this would be my first guess too. $\endgroup$
    – Dandelion
    Commented Dec 4 at 12:59

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